How to call a confirmation dialog box?
When calling an operator via bpy.ops.* without any execution context the execute() method of the respective operator runs by default. If the operator provides any kind of  'user interaction' like a 'confirmation dialog' in this case, then you can pass 'INVOKE_DEFAULT' as execution context when calling the operator which will also run its invoke() method:

bpy.ops.wm.read_homefile('INVOKE_DEFAULT')




In order to display the operator as a button and also 'enable' its user interaction, you have to set the operator_context in the 'layout' before calling the operator:



Blender 2.7x

import bpy

class HelloWorldPanel(bpy.types.Panel):
    """Creates a Panel in the Object properties window"""
    bl_idname = "CUSTOM_my_panel"
    bl_label = "My Panel"
    bl_space_type = "VIEW_3D"
    bl_region_type = "TOOLS"
    bl_category = "Tools"

    def draw(self, context):
        layout = self.layout
        layout.operator_context = 'INVOKE_DEFAULT' #'INVOKE_AREA'
        layout.operator("wm.read_homefile", text="New", icon='NEW')

def register():
    bpy.utils.register_class(HelloWorldPanel)

def unregister():
    bpy.utils.unregister_class(HelloWorldPanel)

if __name__ == "__main__":
    register()


Blender 2.8x

class OBJECT_PT_CustomPanel(bpy.types.Panel):
    bl_label = "My Panel"
    bl_idname = "OBJECT_PT_custom_panel"
    bl_space_type = "VIEW_3D"   
    bl_region_type = "UI"
    bl_category = "Tools"
    bl_context = "objectmode"

    def draw(self, context):
        layout = self.layout
        layout.operator_context = 'INVOKE_DEFAULT' #'INVOKE_AREA'
        layout.operator("wm.read_homefile", text="New", icon='FILE_NEW')

def register():
    bpy.utils.register_class(OBJECT_PT_CustomPanel)

def unregister():
    bpy.utils.unregister_class(OBJECT_PT_CustomPanel)

if __name__ == "__main__":
    register()




Custom Confirm Dialog

For a custom conformation dialog you can wrap the operator into another one and invoke invoke_confirm(operator, event) classmethod of the window-manager to confirm the execution by the user.



Blender 2.7x

import bpy

class SimpleConfirmOperator(bpy.types.Operator):
    """Really?"""
    bl_idname = "my_category.custom_confirm_dialog"
    bl_label = "Do you really want to do that?"
    bl_options = {'REGISTER', 'INTERNAL'}

    @classmethod
    def poll(cls, context):
        return True

    def execute(self, context):
        self.report({'INFO'}, "YES!")
        return {'FINISHED'}

    def invoke(self, context, event):
        return context.window_manager.invoke_confirm(self, event)

class HelloWorldPanel(bpy.types.Panel):
    """Creates a Panel in the Object properties window"""
    bl_idname = "CUSTOM_my_panel"
    bl_label = "My Panel"
    bl_space_type = "VIEW_3D"
    bl_region_type = "TOOLS"
    bl_category = "Tools"

    def draw(self, context):
        layout = self.layout
        layout.operator(SimpleConfirmOperator.bl_idname)

def register():
    bpy.utils.register_class(SimpleConfirmOperator)
    bpy.utils.register_class(HelloWorldPanel)

def unregister():
    bpy.utils.unregister_class(HelloWorldPanel)
    bpy.utils.unregister_class(SimpleConfirmOperator)

if __name__ == "__main__":
    register()


Blender 2.8x

import bpy

class SimpleConfirmOperator(bpy.types.Operator):
    """Really?"""
    bl_idname = "my_category.custom_confirm_dialog"
    bl_label = "Do you really want to do that?"
    bl_options = {'REGISTER', 'INTERNAL'}

    @classmethod
    def poll(cls, context):
        return True

    def execute(self, context):
        self.report({'INFO'}, "YES!")
        return {'FINISHED'}

    def invoke(self, context, event):
        return context.window_manager.invoke_confirm(self, event)


class OBJECT_PT_CustomPanel(bpy.types.Panel):
    bl_label = "My Panel"
    bl_idname = "OBJECT_PT_custom_panel"
    bl_space_type = "VIEW_3D"   
    bl_region_type = "UI"
    bl_category = "Tools"
    bl_context = "objectmode"

    def draw(self, context):
        layout = self.layout
        layout.operator(SimpleConfirmOperator.bl_idname)

def register():
    bpy.utils.register_class(OBJECT_PT_CustomPanel)
    bpy.utils.register_class(SimpleConfirmOperator)

def unregister():
    bpy.utils.unregister_class(SimpleConfirmOperator)
    bpy.utils.unregister_class(OBJECT_PT_CustomPanel)

if __name__ == "__main__":
    register()




Property Confirm

In order to display a popup, some properties and an OK 'button' you can return wm.invoke_props_dialog(self) instead:



Blender 2.7x

import bpy

class SimplePropConfirmOperator(bpy.types.Operator):
    """Really?"""
    bl_idname = "my_category.custom_confirm_dialog"
    bl_label = "Do you really want to do that?"
    bl_options = {'REGISTER', 'INTERNAL'}

    prop1 = bpy.props.BoolProperty()
    prop2 = bpy.props.BoolProperty()

    @classmethod
    def poll(cls, context):
        return True

    def execute(self, context):
        self.report({'INFO'}, "YES!")
        return {'FINISHED'}

    def invoke(self, context, event):
        return context.window_manager.invoke_props_dialog(self)

    def draw(self, context):
        row = self.layout
        row.prop(self, "prop1", text="Property A")
        row.prop(self, "prop2", text="Property B")


class HelloWorldPanel(bpy.types.Panel):
    """Creates a Panel in the Object properties window"""
    bl_idname = "CUSTOM_my_panel"
    bl_label = "My Panel"
    bl_space_type = "VIEW_3D"
    bl_region_type = "TOOLS"
    bl_category = "Tools"

    def draw(self, context):
        layout = self.layout
        layout.operator(SimplePropConfirmOperator.bl_idname)

def register():
    bpy.utils.register_class(SimplePropConfirmOperator)
    bpy.utils.register_class(HelloWorldPanel)

def unregister():
    bpy.utils.unregister_class(HelloWorldPanel)
    bpy.utils.unregister_class(SimplePropConfirmOperator)

if __name__ == "__main__":
    register()


Blender 2.8x

import bpy

class SimplePropConfirmOperator(bpy.types.Operator):
    """Really?"""
    bl_idname = "my_category.custom_confirm_dialog"
    bl_label = "Do you really want to do that?"
    bl_options = {'REGISTER', 'INTERNAL'}

    prop1: bpy.props.BoolProperty()
    prop2: bpy.props.BoolProperty()

    @classmethod
    def poll(cls, context):
        return True

    def execute(self, context):
        self.report({'INFO'}, "YES!")
        return {'FINISHED'}

    def invoke(self, context, event):
        return context.window_manager.invoke_props_dialog(self)

    def draw(self, context):
        row = self.layout
        row.prop(self, "prop1", text="Property A")
        row.prop(self, "prop2", text="Property B")


class OBJECT_PT_CustomPanel(bpy.types.Panel):
    bl_label = "My Panel"
    bl_idname = "OBJECT_PT_custom_panel"
    bl_space_type = "VIEW_3D"   
    bl_region_type = "UI"
    bl_category = "Tools"
    bl_context = "objectmode"

    def draw(self, context):
        layout = self.layout
        layout.operator(SimplePropConfirmOperator.bl_idname)

def register():
    bpy.utils.register_class(OBJECT_PT_CustomPanel)
    bpy.utils.register_class(SimplePropConfirmOperator)

def unregister():
    bpy.utils.unregister_class(SimplePropConfirmOperator)
    bpy.utils.unregister_class(OBJECT_PT_CustomPanel)

if __name__ == "__main__":
    register()


Note: bl_options of both examples are set to 'INTERNAL' which excludes the operators from search results, remove it if you'd like to run the operator via space bar/F3.